Item Type Date No Grouping

2009

SnoopCGH. (2009) Almagro-Garcia, Jacob, Clark, Taane

2012

In Silico Spoligotyping. (2012) Coll, Francesc, Mallard, K, Preston, MD, Bentley, S, Parkhill, Julian, Mcnerney, Ruth, Martin, N, Clark, Taane

VCF Viewer (VARB). (2012) Preston, Mark D., Manske, M, Horner, N, Assefa, S, Campino, S, Auburn, S, Zongo, I, Ouedraogo, JB, Nosten, F, Anderson, T, Clark, Taane

20 August 2012

Tuberculosis Patients Blood Gene Expression Through Treatment. (2012) Cliff, Jackie, Lee, Ji-Sook, Constantinou, Nicholas, Cho, Jang-Eun, Clark, Taane G., Ronacher, Katharina, King, Elizabeth C., Lukey, Pauline T., Duncan, Ken, Van Helden, Paul D., Walzl, Gerhard, Dockrell, Hazel M.

Tuberculosis Patients Blood Gene Expression Through Treatment (cured and end-of-treatment patients). (2012) Cliff, Jackie, Lee, Ji-Sook, Constantinou, Nicholas, Cho, Jang-Eun, Clark, Taane G., Ronacher, Katharina, King, Elizabeth C., Lukey, Pauline T., Duncan, Ken, Van Helden, Paul D., Walzl, Gerhard, Dockrell, Hazel M.

2014

Data for: "A robust SNP barcode for typing Mycobacterium tuberculosis complex strains". (2014) Coll, Francesc, Mcnerney, Ruth, Guerra-Assunção, José Afonso, Glynn, Judith R., Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Pain, Arnab, Martin, Nigel, Clark, Taane G. description

May 2014

PolyTB: A web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale. (2014) Coll, Francesc, Preston, Mark, Guerra-Assunção, José Afonso, Hill-Cawthorn, Grant, Harris, David, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Drobniewski, Francis, Gagneux, Sebastien, Glynn, Judith R., Pain, Arnab, Parkhill, Julian, McNerney, Ruth, Martin, Nigel, Clark, Taane

2015

TB Profiler. (2015) Coll, Francesc, Mcnerney, Ruth, Preston, Mark D., Guerra-assunção, José Afonso, Warry, Andrew, Hill-Cawthorne, Grant, Mallard, Kim, Nair, Mridul, Miranda, Anabela, Alves, Adriana, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Hasan, Zahra, Hasan, Rumina, Glynn, Judith, Martin, Nigel, Pain, Arnab, Clark, Taane folder_zip

18 March 2015

Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity: Supplementary data. (2015) Mobegi, Victor, Duffy, Craig, Amambua-Ngwa, Alfred, Loua, Kovana M, Laman, Eugene, Nwakanma, Davis C, MacInnis, Bronwyn, Aspeling-jones, Harvey, Murray, Lee, Clark, Taane, Kwiatkowski, Dominic P, Conway, David grid_on

26 March 2015

PhyloTrack. (2015) Benavente, Ernest, Coll, Francesc, Furnham, Nick, Mcnerney, Ruth, Glynn, Judith, Campino, Susana, Pain, Arnab, Mohareb, Fady R, Clark, Taane

15 October 2015

Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia. (2015) Getachew, Sisay, To, Sheren, Trimarsanto, Hidayat, Thriemer, Kamala, Clark, Taane, Petros, Beyene, Aseffa, Abraham, Price, Ric N, Auburn, Sarah grid_on

4 November 2015

Whole genome sequences for M.tuberculosis isolates from the TDR strain bank. (2015) Phelan, Jody, Coll, Francesc, Mcnerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin, Pain, Arnab, Rigouts, Leen, Clark, Taane description

1 January 2016

Mycobacterium tuberculosis Nonthaburi genotype raw reads. (2016) Coker, Olabisi Oluwabukola, Chaiprasert, Angkana, Ngamphiw, Chumpol, Tongsima, Sissades, Regmi, Sanjib Mani, Clark, Taane, Ong, Rick Twee Hee, Teo, Yik-Ying, Prammananan, Therdsak, Palittapongarnpim, Prasit

5 July 2016

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species. (2016) Ansari, Hifzur Rahman, Templeton, Thomas J., Subudhi, Amit Kumar, Ramaprasad, Abhinay, Tang, Jianxia, Lu, Feng, Naeem, Raeece, Hashish, Yasmeen, Oguike, Mary C., Benavente, Ernest Diez, Clark, Taane G., Sutherland, Colin J., Barnwell, John W., Culleton, Richard, Cao, Jun, Pain, Arnab

8 February 2017

Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. (2017) Andreu, Nuria, Phelan, Jody, de Sessions, Paola F, Cliff, Jackie M., Clark, Taane, Hibberd, Martin

22 September 2017

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations. (2017) Diez Benavente, Ernest, Florez de Sessions, Paola, Moon, Robert W., Holder, Anthony A., Blackman, Michael J., Roper, Cally, Drakeley, Christopher J., Pain, Arnab, Sutherland, Colin J., Hibberd, Martin L., Campino, Susana, Clark, Taane G.

2 May 2018

Global analysis of Plasmodium falciparum histidine-rich protein-2 ( pfhrp2 ) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. (2018) Sepúlveda, Nuno, Phelan, Jody, Diez-Benavente, Ernest, Campino, Susana, Clark, Taane G., Hopkins, Heidi, Sutherland, Colin, Drakeley, Chris J., Beshir, Khalid B.

2 August 2018

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. (2018) Palittapongarnpim, Prasit, Ajawatanawong, Pravech, Viratyosin, Wasna, Smittipat, Nat, Disratthakit, Areeya, Mahasirimongkol, Surakameth, Yanai, Hideki, Yamada, Norio, Nedsuwan, Supalert, Imasanguan, Worarat, Kantipong, Pacharee, Chaiyasirinroje, Boonchai, Wongyai, Jiraporn, Toyo-oka, Licht, Phelan, Jody, Parkhill, Julian, Clark, Taane G., Hibberd, Martin L., Ruengchai, Wuthiwat, Palittapongarnpim, Panawun, Juthayothin, Tada, Tongsima, Sissades, Tokunaga, Katsushi

14 August 2018

Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. (2018) Sobkowiak, Benjamin, Glynn, Judith R., Houben, Rein M. G. J., Mallard, Kim, Phelan, Jody E., Guerra-Assunção, José Afonso, Banda, Louis, Mzembe, Themba, Viveiros, Miguel, McNerney, Ruth, Parkhill, Julian, Crampin, Amelia C., Clark, Taane G.

24 June 2019

Additional file 1: of Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. (2019) Phelan, Jody, O’Sullivan, Denise M, Machado, Diana, Ramos, Jorge, Oppong, Yaa EA, Campino, Susana, O’Grady, Justin, McNerney, Ruth, Hibberd, Martin L, Viveiros, Miguel, Huggett, Jim F, Clark, Taane G.

15 December 2020

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype. (2020) Srilohasin, Prapaporn, Prammananan, Therdsak, Faksri, Kiatichai, Phelan, Jody E., Suriyaphol, Prapat, Kamolwat, Phalin, Smithtikarn, Saijai, Disratthakit, Areeya, Regmi, Sanjib Mani, Leechawengwongs, Manoon, Twee-Hee Ong, Rick, Teo, Yik Ying, Tongsima, Sissades, Clark, Taane G., Chaiprasert, Angkana

11 May 2021

Study database for: "Adverse pregnancy outcomes are associated with Plasmodium vivax malaria in a prospective cohort of women from the Brazilian Amazon". (2021) Fuehrer, Hans-Peter, Dombrowski, Jamille Gregório, Barateiro, André, Peixoto, Erika Paula Machado, Barros, André Boler Cláudio da Silva, Souza, Rodrigo Medeiros de, Clark, Taane Gregory, Campino, Susana, Wrenger, Carsten, Wunderlich, Gerhard, Palmisano, Giuseppe, Epiphanio, Sabrina, Gonçalves, Lígia Antunes, Marinho, Claudio Romero Farias

27 June 2021

Data for: "Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus". (2021) Spadar, Anton, Phelan, Jody, Diez-Benavente, Ernest, Campos, Monica, Gomez, Lara Ferrero, Mohareb, Fady, Clark, Taane G., Campino, Susana

10 November 2021

Getting close to nature – Plasmodium knowlesi reference genome sequences from contemporary clinical isolates. (2021) Damilola R. Oresegun, Peter Thorpe, Benavente, Ernest, Campino, Susana, Fauzi Muh, Moon, Robert W., Clark, Taane, Cox-Singh, Janet

24 December 2021

Table_1_Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq.XLSX. (2021) Gibson, Amanda J., Passmore, Ian J., Faulkner, Valwynne, Xia, Dong, Nobeli, Irene, Stiens, Jennifer, Willcocks, Sam, Clark, Taane G., Sobkowiak, Ben, Werling, Dirk, Villarreal-Ramos, Bernardo, Wren, Brendan W., Kendall, Sharon L.

17 February 2022

A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. (2022) Eccleston, R. Charlotte, Manko, Emilia, Campino, Susana, Clark, Taane G., Furnham, Nicholas

23 May 2022

De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members. (2022) Oresegun, Damilola R., Thorpe, Peter, Benavente, Ernest Diez, Campino, Susana, Muh, Fauzi, Moon, Robert William, Clark, Taane Gregory, Cox-Singh, Janet

13 April 2023

Additional file 2 of Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains. (2023) Spadar, Anton, Perdigão, João, Campino, Susana, Clark, Taane G.

13 August 2024

Additional file 1 of Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. (2024) Spadar, Anton, Phelan, Jody, Clark, Taane G., Campino, Susana

Additional file 3 of Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. (2024) Spadar, Anton, Phelan, Jody E., Clark, Taane G., Campino, Susana